South Sudanese women displaced by the fighting wait in line for personal hygiene kits in a camp for the displaced, inside the United Nations compound in Bor, March 15, 2014. A pro-government militia attacked a UN base in Bor on Thursday, April 17, where some 5,000 civilians were sheltering from the civil war.

Andreea Campeanu/Reuters/File

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Nairobi, Kenya

Scores of civilians were killed Thursday and more than 100 were injured when an armed youth militia attacked a United Nations base in the South Sudan town of Bor, where some 5,000 civilians were sheltering from the civil war.

The attackers, claiming to be peaceful demonstrators, ignored peacekeepers’ warning shots and breached security fences to spray bullets at civilians inside before the "blue helmets," as UN forces are often known, forced them out.

It was the deadliest incident at a UN base in the four-month conflict, which began in December when the Army split along ethnic lines in a political struggle between President Salva Kiir, a Dinka, and his rival Riek Machar, a Nuer. Thousands of people have been killed, and over a million have fled their homes, including 75,000 taking refuge in UN bases across the country.

Thursday's killings mark a low point in South Sudan for the UN, which has faced continual accusations from the government of siding with the rebels. The Bor incident is also the first attack by a pro-government civilian militia, perhaps marking a new and dangerous phase of the fighting.

“I think this is reaching another level of conflict that I hoped would be avoided,” says Jok Madut Jok, director of the Sudd Institute, a Juba think tank. He adds that recent rebel victories may be driving an armed Dinka populace to take a more aggressive role. Bor, the riverside capital of hard-fought-for Jonglei State, has changed hands repeatedly but has been in government control since January.

High death toll

A UN official in the Bor base told the Monitor by phone Friday morning that he “visually confirmed” more than 40 dead civilians, and that nearly 100 were injured. At Bor's hospital, outside the compound, Dr. Ayool G Ayool said by phone that he signed death certificates of 10 people – presumably attackers – shot by peacekeepers, and warned the death toll could rise.

Toby Lanzer, the UN humanitarian chief for South Sudan, said he was “outraged” by the attack, adding “we will not be deterred.”

The UN has struggled to maintain its image in South Sudan during the war. At the heart of the problem, and apparently the cause of Thursday’s attack, is the idea that UN bases are sheltering members of the White Army, a rebel-aligned Nuer militia accused of committing atrocities against Dinka civilians.

The UN will protect any unarmed person in civilian clothes. In Bor, many Dinka say rebels dropped their weapons and entered the UN base once the government retook the town. Earlier this week, Nuer civilians in the UN base in Bentiu loudly celebrated the rebel takeover there, firming up perceptions that UN-protected civilians include rebel sympathizers or former militants.

“Basically they were objecting to the presence of White Army people within the Protection of Civilians area [in the base],” the UN source in Bor said of Thursday’s attackers.

South Sudan has accused the UN of running a “parallel state” in its compounds. An attempt in January by a government minister to enter Bor’s base with armed bodyguards—a UN protocol violation— fueled further distrust.

In March, South Sudan’s Army found weapons in a mislabeled shipment of UN goods. The UN said it was a mistake, but the government accused them of trying to arm rebels, and organized street protests against the UN. The UN then released a report accusing the South Sudanese Army of harassing its staff.

“The situation has gotten to a point where there cannot be any trust between the leaders in the government at the moment and the local UN,” says Mr. Jok, at the Sudd Institute. “Now the UN is increasingly having that [negative] image not just by the government, but the people who support the government. The result of this tense relationship just manifested itself yesterday. ”

The attack on Nuer civilians in Bor has deeply shaken their confidence in the UN’s ability to protect them.

“We think they will come again and attack,” William Tut, the Bor camp civilian chairman, says by phone. “They see that there is nothing stopping them.”